Commit 5982f45b authored by Andreas Tille's avatar Andreas Tille
Browse files

Package only Python version, provide example data in examples package

parent df17d7f7

debian/README.Debian

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resfinder for Debian

====================



Quoting the resfinder doc:



    The ResFinder service contains one perl script *resfinder.pl* which is the

    script of the latest version of the ResFinder service. ResFinder identifies

    acquired antimicrobial resistance genes in total or partial sequenced isolates

    of bacteria.



    This repository also contains a python script *resfinder.py* which is  a new version

    of ResFinder, but not yet running on the CGE server. This program was added because

    it uses a newer version of blastn,  which, in contrary from the blastall version

    that the perl script uses, is avail to download.



The user who requested this package is just interested in the Python version of

redfinder thus only this script is packaged.





 -- Andreas Tille <tille@debian.org>  Thu, 07 Nov 2019 12:41:11 +0100

debian/changelog

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resfinder (3.2-1) UNRELEASED; urgency=medium



  * Initial release (Closes: #<bug>)

  TODO: Clarify relation between *.pl and *.py



 -- Andreas Tille <tille@debian.org>  Thu, 07 Nov 2019 12:41:11 +0100

debian/control

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@@ -4,16 +4,16 @@ Uploaders: Andreas Tille <tille@debian.org> 
Section: science

Priority: optional

Build-Depends: debhelper-compat (= 12),

               dh-python

               dh-python,

               python3

Standards-Version: 4.4.1

Vcs-Browser: https://salsa.debian.org/med-team/resfinder

Vcs-Git: https://salsa.debian.org/med-team/resfinder.git

Homepage: https://bitbucket.org/genomicepidemiology/resfinder



Package: resfinder

Architecture: any

Depends: ${perl:Depends},

         ${python3:Depends},

Architecture: all

Depends: ${python3:Depends},

         ${misc:Depends},

         bioperl,

         ncbi-blast+-legacy
@@ -27,3 +27,20 @@ Description: identifies acquired antimicrobial resistance genes 
 from four different sequencing platforms. The method was evaluated on

 1862 GenBank files containing 1411 different resistance genes, as well

 as on 23 de-novo-sequenced isolates.



Package: resfinder-example

Architecture: all

Depends: ${misc:Depends},

Recommends: resfinder

Description: identifies acquired antimicrobial resistance genes (example data)

 ResFinder identifies acquired antimicrobial resistance genes in total or

 partial sequenced isolates of bacteria.

 .

 ResFinder that uses BLAST for identification of acquired antimicrobial

 resistance genes in whole-genome data. As input, the method can use both

 pre-assembled, complete or partial genomes, and short sequence reads

 from four different sequencing platforms. The method was evaluated on

 1862 GenBank files containing 1411 different resistance genes, as well

 as on 23 de-novo-sequenced isolates.

 .

 This package contains example data to test resfinder.

debian/install

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*.py	/usr/bin

*.pl	/usr/bin

debian/lintian-overrides

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# see discussion on Debian Med mailing list

#   https://lists.debian.org/debian-med/2018/06/msg00042.html

# and following mails in thread

resfinder: script-with-language-extension usr/bin/resfinder.pl
 
resfinder: script-with-language-extension usr/bin/resfinder.py